Many years prior to the start of the game, Admiral Bobbery was infatuated with a Bob-omb named Scarlette. He loved her madly and proudly, only matched by his love of the sea. A renowned sailor, Admiral Bobbery spent most of his time traveling on the oceans, and Scarlette would patiently await his return.

One particularly icy winter, Scarlette fell ill while Admiral Bobbery was out at sea. Her condition rapidly deteriorated, and by the time Bobbery returned, she was dead. Aghast and deeply saddened, Admiral Bobbery blamed himself for Scarlette's death, thinking that he could have nursed her back to health had he been there. Tormented by nightmares of Scarlette, Bobbery eventually vowed to never sail again out of guilt for his perceived failure to his beloved.

Unbeknownst to Bobbery, Scarlette gave Podley an Old Letter prior to her death, telling him to give it to her beloved. Podley agreed to her last request, but found himself unable to do it when he saw how depressed Bobbery was. Nonetheless, he tried to help his old friend however he could. When introduced in Chapter 5, Admiral Bobbery appears to have settled down in Rogueport, drowning his grief in the bar.

Needing a navigator to get to Keelhaul Key, Mario meets up with Admiral Bobbery, who denies his identity. After checking with Professor Frankly, Mario returns to renew his request to the old sailor; he admits that he is Admiral Bobbery, but still refuses to help.

Further advice from Professor Frankly sends Mario to Podley's Place. After hearing Admiral Bobbery's depressing tale, Mario receives the Old Letter from Podley, who requests that Mario give it to Bobbery. Upon reading the letter, which contains Scarlette's encouragement for him to embrace his other love of the sea, Admiral Bobbery agrees to join Mario.

However, the ship is attacked by Embers during the voyage and sinks; when the survivors wash up on the shores of Keelhaul Key, Bobbery is declared missing along with Four-Eyes and a Toad. The three are found soon after by Mario during an island exploration, once again being attacked by the pirate ghosts - the admiral makes a heroic sacrifice by distracting the ghosts and allowing the others to escape back to camp.

Venturing into the jungle once more leads the player to a near-death Bobbery, who thanks Mario for convincing him to take one last voyage out to sea before requesting a bottle of his favorite drink - Chuckola Cola - as his last wish. After exchanging a Coconut with Flavio for the drink and returning it to Bobbery, he consumes it and presumably passes on. However, it is quickly made apparent that the admiral is only asleep rather than dead - after a 'wake-up whack' from Mario's hammer, Bobbery joins the plumber's team as his next party member.

A retired Bob-omb sea captain, Admiral Bobbery assists Mario in his quest with his bomb-related attacks and abilities. Outside of battle, he uses the same attack as Bombette from Paper Mario to explode and blow up cracks. However, unlike Admiral Bobbery's counterpart, he can be thrown onto high ledges to explode. Also, her main move is a Body Slam and blowing up costs FP, though it's her FP standard but Bobbery's main move is blowing up and his FP standard is throwing time bombs.

The admiral also proves useful when Mario and co. visit Fahr Outpost in search of the cannon that can shoot them to the moon, as he helps to improve relations between Mario and the resident Bob-ombs and explains their situation to the mayor. It is during this sequence that Bobbery reveals he once visited the outpost before, though the details of the trip are never given.

After defeating the Shadow Queen, Admiral Bobbery joins Cortez and sails the seas with him.

(Rogueport) That's Admiral Bobbery. All the dock workers call him a legendary helmsman. I don't know if that's true, but he definitely seems like the most capable sailor here! I know he's been through a lot, but I'm glad we brought him around, aren't you?

(Keelhaul Key) That's Admiral Bobbery. He came with us on the ship, don't you remember? He washed ashore with the rest of us... but he seems hurt. You think he's doing OK?

The picture to the right could be an early design of Admiral Bobbery before his sailor design was made. This Admiral Bobbery resembles a soldier more than a sailor and can be found within the game's sprite resources.

Out of all the partners in the game, Admiral Bobbery has the highest HP total.

Admiral Bobbery is the only character who doesn't go to sleep during Luigi's stories.